Starr: Simple Tiling Array Analysis of Affymetrix ChIP-chip data

Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay for DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires a thorough bioinformatic processing of the data for which there is no standard yet. The primary goal is the reliable identification and localization of genomic regions that bind a specific protein. The second step comprises comparison of binding profiles of functionally related proteins, or of binding profiles of the same protein in different genetic backgrounds or environmental conditions. Ultimately, one would like to gain a mechanistic understanding of the effects of DNA binding events on gene expression. We present a free, open-source R package Starr that, in combination with the package Ringo, facilitates the comparative analysis of ChIP-chip data across experiments and across different microarray platforms. Core features are data import, quality assessment, normalization and visualization of the data, and the detection of ChIP-enriched genomic regions. The use of common Bioconductor classes ensures the compatibility with other R packages. Most importantly, Starr provides methods for integration of complementary genomics data, e.g., it enables systematic investigation of the relation between gene expression and dna binding

Structure Learning in Nested Effects Models

Nested Effects Models (NEMs) are a class of graphical models introduced to analyze the results of gene perturbation screens. NEMs explore noisy subset relations between the high-dimensional outputs of phenotyping studies, e.g. the effects showing in gene expression profiles or as morphological features of the perturbed cell. In this paper we expand the statistical basis of NEMs in four directions: First, we derive a new formula for the likelihood function of a NEM, which generalizes previous results for binary data. Second, we prove model identifiability under mild assumptions. Third, we show that the new formulation of the likelihood allows to efficiently traverse model space. Fourth, we incorporate prior knowledge and an automated variable selection criterion to decrease the influence of noise in the data

Selective phenotyping, entropy reduction, and the mastermind game.

BACKGROUND: With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. RESULTS: Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset. CONCLUSIONS: Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping

Technological World-Pictures: Cosmic Things and Cosmograms

Martin Heidegger’s notion of things as gatherings that disclose a world conveys the “thickness” of everyday objects. This essay extends his discussion of things—part of a sustained criticism of modern technology—to technological objects as well. As a corrective to his totalizing, even totalitarian, generalizations about “enframing” and “the age of the world‐picture,” and to a more widespread tendency among critics of modernity to present technology in only the most dystopian, uniform, and claustrophobic terms, this essay explores two species of technical object: cosmic things and cosmograms. The first suggests how an ordinary object may contain an entire cosmos, the second how a cosmos may be treated as just another thing. These notions are proposed as a basis for comparison and connection between “the industrial world” and other modes of ordering the universe

The Prophet and the Pendulum: Sensational Science and Audiovisual Phantasmagoria Around 1848

During the French Second Republic—the volatile period between the 1848 Revolution and Louis-Napoléon Bonaparte’s 1851 coup d’état—two striking performances fired the imaginations of Parisian audiences. The first, in 1849, was a return: after more than a decade, the master of the Parisian grand opera, Giacomo Meyerbeer, launched Le prophète, whose complex instrumentation and astounding visuals—including the unprecedented use of electric lighting—surpassed even his own previous innovations in sound and vision. The second, in 1851, was a debut: the installation of Foucault’s pendulum in the Panthéon. The installation marked the first public exposure of one of the most celebrated demonstrations in the history of science. A heavy copper ball suspended from the former cathedral’s copula, once set in motion, swung in a plane that slowly traced a circle on the marble floor, demonstrating the rotation of the earth

Toward a New Organology: Instruments of Music and Science

The Renaissance genre of organological treatises inventoried the forms and functions of musical instruments. This article proposes an update and expansion of the organological tradition, examining the discourses and practices surrounding both musical and scientifi c instruments. Drawing on examples from many periods and genres, we aim to capture instruments’ diverse ways of life. To that end we propose and describe a comparative “ethics of instruments”: an analysis of instruments’ material configurations, social and institutional locations, degrees of freedom, and teleologies. This perspective makes it possible to trace the intersecting and at times divergent histories of science and music: their shared material practices, aesthetic commitments, and attitudes toward technology, as well as their impact on understandings of human agency and the order of nature

Low-energy muon-transfer reaction from hydrogen isotopes to helium isotopes

Direct muon transfer in low-energy collisions of the muonic hydrogen H$_\mu$ and helium (He$^{++}$) is considered in a three-body quantum-mechanical framework of coordinate-space integro-differential Faddeev-Hahn-type equations within two- and six-state close coupling approximations. The final-state Coulomb interaction is treated without any approximation employing appropriate Coulomb waves in the final state. The present results agree reasonably well with previous semiclassical calculations.Comment: 4 revtex4 page